Investigations of the pathogenesis of JC Virus induced progressive leukoencephalopathy (PML) focus on mechanisms of latency of JCV in human tissues, viral activation and transport to the brain and transcriptional control of viral gene expression. Experiments are conducted at the clinical, biological and molecular levels. Using PCR analysis, JCV from suspected latently infected lymphocytes in bone marrow has been found in peripheral lymphocytes in more than 90% of PML patients, particularly individuals with AIDS as the underlying immune disorder. JCV DNA was also found in greater than 50% of immune suppressed individuals without PML identifying them at risk for the development of PML. DNA sequence analysis of the regulatory region from several PML patients demonstrated the prototype (two 98 base pair repeat units) sequence arrangement in peripheral blood but a greatly rearranged DNA sequence in the brain. JCV DNA was also found for the first time in a Wiskott/Aldrich syndrome patient in biopsies of bone marrow and brain, and in bone marrow and kidney tissues taken three years prior to PML at the time of therapeutic splenectomy. This unique case study of PML highlights the observation of JCV latency in marrow cells of the marrow. These results suggest that JCV could be spread to the CNS by a hematogenous route, possibly through a B lymphocyte vector. To examine molecular control of viral expression, nuclear proteins from human fetal brain and human B cells were examined for their ability to bind to the JCV regulatory region. A protein factor(s) from both of these sources was able to bind several sites which contain the recognition sequence for a NF-1 protein. A c-jun like factor was also able to bind the regulatory region. The NF-1 and c-jun binding sites were either adjacent or overlapped each other. Examination of the regulatory regions of many other genes expressed in the brain such as MBP, GFAP, PLP, S100B, NF-L, and pro-ENK revealed that they also appear to contain adjacent binding sites for NF- 1 and an activator protein immediately upstream from the mRNA start site. These results suggest that they share common factors which regulate these genes in a tissue-specific manner.